Published in Genome Res on December 07, 2011
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
The MaSuRCA genome assembler. Bioinformatics (2013) 5.07
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86
Exploiting sparseness in de novo genome assembly. BMC Bioinformatics (2012) 2.88
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda) (2013) 2.85
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics (2012) 2.46
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol (2014) 2.44
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res (2013) 2.43
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24
A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Res (2013) 2.08
The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell (2015) 1.86
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Res (2012) 1.76
Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One (2014) 1.74
In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc Natl Acad Sci U S A (2015) 1.72
Current challenges in de novo plant genome sequencing and assembly. Genome Biol (2012) 1.69
AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PLoS One (2015) 1.65
Computational solutions for omics data. Nat Rev Genet (2013) 1.58
A comprehensive evaluation of assembly scaffolding tools. Genome Biol (2014) 1.55
The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol (2013) 1.54
Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism. Curr Biol (2015) 1.52
GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One (2014) 1.49
The TIR Homologue Lies near Resistance Genes in Staphylococcus aureus, Coupling Modulation of Virulence and Antimicrobial Susceptibility. PLoS Pathog (2017) 1.39
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife (2015) 1.36
Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput Biol (2014) 1.36
Exploring genome characteristics and sequence quality without a reference. Bioinformatics (2014) 1.34
Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics (2014) 1.33
Next-generation sequencing and large genome assemblies. Pharmacogenomics (2012) 1.27
Postglacial viability and colonization in North America's ice-free corridor. Nature (2016) 1.26
Reference-assisted chromosome assembly. Proc Natl Acad Sci U S A (2013) 1.26
Genetic variation and the de novo assembly of human genomes. Nat Rev Genet (2015) 1.24
Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun (2014) 1.24
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol (2014) 1.24
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform (2015) 1.22
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res (2016) 1.20
The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet (2015) 1.19
Comprehensive variation discovery in single human genomes. Nat Genet (2014) 1.18
Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol (2015) 1.17
Data compression for sequencing data. Algorithms Mol Biol (2013) 1.13
Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics (2012) 1.12
A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12
Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res (2014) 1.11
The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet (2016) 1.09
Telescoper: de novo assembly of highly repetitive regions. Bioinformatics (2012) 1.08
Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol (2013) 1.07
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics (2014) 1.04
The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol (2016) 1.02
Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions. Int J Parasitol Drugs Drug Resist (2014) 1.02
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nat Genet (2014) 1.02
QuorUM: An Error Corrector for Illumina Reads. PLoS One (2015) 0.99
BFC: correcting Illumina sequencing errors. Bioinformatics (2015) 0.99
The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet (2013) 0.96
Using the Sadakane compressed suffix tree to solve the all-pairs suffix-prefix problem. Biomed Res Int (2014) 0.92
Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PLoS One (2013) 0.92
Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks. Genome Biol Evol (2015) 0.91
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. Microb Genom (2017) 0.91
DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci Rep (2016) 0.91
Near-optimal assembly for shotgun sequencing with noisy reads. BMC Bioinformatics (2014) 0.90
Fast construction of FM-index for long sequence reads. Bioinformatics (2014) 0.90
Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biol Evol (2014) 0.89
Assembler for de novo assembly of large genomes. Proc Natl Acad Sci U S A (2013) 0.89
Identification of structural variation in mouse genomes. Front Genet (2014) 0.88
Drug resistance analysis by next generation sequencing in Leishmania. Int J Parasitol Drugs Drug Resist (2014) 0.87
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics (2013) 0.86
Evaluating de Bruijn graph assemblers on 454 transcriptomic data. PLoS One (2012) 0.86
A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework. BMC Genomics (2012) 0.86
The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biol (2014) 0.86
The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome. Sci Rep (2015) 0.86
The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol (2016) 0.83
Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha. BMC Genomics (2014) 0.83
Pollux: platform independent error correction of single and mixed genomes. BMC Bioinformatics (2015) 0.82
PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach. PLoS One (2014) 0.82
SAGE: String-overlap Assembly of GEnomes. BMC Bioinformatics (2014) 0.82
A brief overview of the size and composition of the myrtle rust genome and its taxonomic status. Mycology (2014) 0.82
Quality control of next-generation sequencing data without a reference. Front Genet (2014) 0.82
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters! PLoS One (2017) 0.82
Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res (2015) 0.81
Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genome Med (2015) 0.81
Comparative transcriptome analysis of four prymnesiophyte algae. PLoS One (2014) 0.81
The genome landscape of the african green monkey kidney-derived vero cell line. DNA Res (2014) 0.81
A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PLoS Comput Biol (2014) 0.81
Compact representation of k-mer de Bruijn graphs for genome read assembly. BMC Bioinformatics (2013) 0.81
Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes. Genome Res (2016) 0.81
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics (2013) 0.81
The sil Locus in Streptococcus Anginosus Group: Interspecies Competition and a Hotspot of Genetic Diversity. Front Microbiol (2017) 0.81
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. Brief Bioinform (2016) 0.80
Genome-scale sequencing to identify genes involved in Mendelian disorders. Curr Protoc Hum Genet (2013) 0.80
De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms. Front Microbiol (2014) 0.80
Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA. DNA Res (2013) 0.80
Merging of multi-string BWTs with applications. Bioinformatics (2014) 0.80
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics (2016) 0.80
TIGER: tiled iterative genome assembler. BMC Bioinformatics (2012) 0.80
Konnector v2.0: pseudo-long reads from paired-end sequencing data. BMC Med Genomics (2015) 0.80
HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads. BMC Genomics (2016) 0.80
Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Res (2016) 0.80
SeedsGraph: an efficient assembler for next-generation sequencing data. BMC Med Genomics (2015) 0.79
De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PLoS One (2014) 0.79
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Genome sequence of the nematode C. elegans: a platform for investigating biology. Science (1998) 61.48
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Short read fragment assembly of bacterial genomes. Genome Res (2007) 15.40
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
The fragment assembly string graph. Bioinformatics (2005) 11.84
The case for cloud computing in genome informatics. Genome Biol (2010) 9.20
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered (2009) 7.18
Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol (2010) 6.38
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
Efficient construction of an assembly string graph using the FM-index. Bioinformatics (2010) 4.13
HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics (2010) 3.58
Real-time DNA sequencing from single polymerase molecules. Methods Enzymol (2010) 3.34
Succinct data structures for assembling large genomes. Bioinformatics (2011) 2.03
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature (2003) 26.58
The variant call format and VCFtools. Bioinformatics (2011) 25.88
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
GeneWise and Genomewise. Genome Res (2004) 17.87
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
Ensembl 2011. Nucleic Acids Res (2010) 14.68
Ensembl 2012. Nucleic Acids Res (2011) 14.55
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Prepublication data sharing. Nature (2009) 12.24
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
An overview of Ensembl. Genome Res (2004) 10.35
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics (2002) 9.36
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Dindel: accurate indel calls from short-read data. Genome Res (2010) 8.62
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Inference of human population history from individual whole-genome sequences. Nature (2011) 8.05
The DNA sequence of the human X chromosome. Nature (2005) 6.97
Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet (2012) 6.97
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51
Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci U S A (2003) 6.01
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95
Patterns of cis regulatory variation in diverse human populations. PLoS Genet (2012) 5.28
WormBase: a cross-species database for comparative genomics. Nucleic Acids Res (2003) 5.28
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (2010) 4.69
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
Efficient construction of an assembly string graph using the FM-index. Bioinformatics (2010) 4.13
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Mapping trait loci by use of inferred ancestral recombination graphs. Am J Hum Genet (2006) 4.01
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
The UK10K project identifies rare variants in health and disease. Nature (2015) 3.89
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
WormBase 2007. Nucleic Acids Res (2007) 3.69
Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet (2012) 3.56
A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol (2010) 3.23
Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics (2002) 2.99
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res (2010) 2.97
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Trait variation in yeast is defined by population history. PLoS Genet (2011) 2.50
Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res (2011) 2.42
GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res (2002) 2.20
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc (2012) 2.14
A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10
Enhanced protein domain discovery using taxonomy. BMC Bioinformatics (2004) 1.81
High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics (2013) 1.72
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol (2012) 1.68
The anatomy of successful computational biology software. Nat Biotechnol (2013) 1.68
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol (2007) 1.63
A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res (2004) 1.60
Copy number variant detection in inbred strains from short read sequence data. Bioinformatics (2009) 1.45
Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res (2004) 1.43
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol (2009) 1.43
Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol (2013) 1.34
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. Proc Natl Acad Sci U S A (2007) 1.33
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol (2007) 1.29
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet (2012) 1.28
Joint genetic analysis of gene expression data with inferred cellular phenotypes. PLoS Genet (2011) 1.26
Extending reference assembly models. Genome Biol (2015) 1.06
Identity-by-descent-based phasing and imputation in founder populations using graphical models. Genet Epidemiol (2011) 1.05
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure. Bioinformatics (2007) 0.99
Vertebrate gene finding from multiple-species alignments using a two-level strategy. Genome Biol (2006) 0.99
WormBase: Annotating many nematode genomes. Worm (2012) 0.91
A genome-wide survey of genetic variation in gorillas using reduced representation sequencing. PLoS One (2013) 0.78
A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes. RNA (2006) 0.78
Erratum: Whole-genome sequence-based analysis of thyroid function. Nat Commun (2015) 0.77
Inferring selection on amino acid preference in protein domains. Mol Biol Evol (2008) 0.77
A table-driven, full-sensitivity similarity search algorithm. J Comput Biol (2003) 0.77
Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet (2015) 0.75
[X]uniqMAP: unique gene sequence regions in the human and mouse genomes. BMC Genomics (2006) 0.75
Erratum: A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans. Nat Commun (2015) 0.75
Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature (2017) 0.75