All Your Base: a fast and accurate probabilistic approach to base calling.


:The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base calling method which improves on the best existing base callers, especially when comparing the number of error-free reads. The novel algorithms implemented in All Your Base (AYB) are comparable in speed to other competitive base-calling methods, do not require training data and are designed to be robust to gross errors, producing sensible results where other techniques struggle. AYB is available at


Genome Biol


Genome biology


Massingham T,Goldman N




Has Abstract


2012-02-29 00:00:00














  • Most partial domains in proteins are alignment and annotation artifacts.

    abstract:BACKGROUND:Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Triant DA,Pearson WR

    更新日期:2015-05-15 00:00:00

  • Genomes of uncultured eukaryotes: sorting FACS from fiction.

    abstract::A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Worden AZ,Dupont C,Allen AE

    更新日期:2011-06-27 00:00:00

  • Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

    abstract:BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Brochier C,Gribaldo S,Zivanovic Y,Confalonieri F,Forterre P

    更新日期:2005-01-01 00:00:00

  • A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

    abstract:BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we deve...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Moore JE,Pratt HE,Purcaro MJ,Weng Z

    更新日期:2020-01-22 00:00:00

  • iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations.

    abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Henry CS,Zinner JF,Cohoon MP,Stevens RL

    更新日期:2009-01-01 00:00:00

  • Why genomics is more than genomes.

    abstract::A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004. ...

    journal_title:Genome biology



    authors: Lawrence JG

    更新日期:2004-01-01 00:00:00

  • Concept recognition for extracting protein interaction relations from biomedical text.

    abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

    更新日期:2008-01-01 00:00:00

  • Studying the microbiology of the indoor environment.

    abstract::The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Kelley ST,Gilbert JA

    更新日期:2013-02-28 00:00:00

  • Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.

    abstract:BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

    更新日期:2020-07-02 00:00:00

  • Searching for SNPs with cloud computing.

    abstract::As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

    更新日期:2009-01-01 00:00:00

  • Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.

    abstract:BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Quick J,Ashton P,Calus S,Chatt C,Gossain S,Hawker J,Nair S,Neal K,Nye K,Peters T,De Pinna E,Robinson E,Struthers K,Webber M,Catto A,Dallman TJ,Hawkey P,Loman NJ

    更新日期:2015-05-30 00:00:00

  • GNB5 mutation causes a novel neuropsychiatric disorder featuring attention deficit hyperactivity disorder, severely impaired language development and normal cognition.

    abstract:BACKGROUND:Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanis...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Shamseldin HE,Masuho I,Alenizi A,Alyamani S,Patil DN,Ibrahim N,Martemyanov KA,Alkuraya FS

    更新日期:2016-09-27 00:00:00

  • The Smads.

    abstract:SUMMARY:The large transforming growth factor-beta (TGFbeta) superfamily of secreted proteins regulate the growth, development and differentiation of cells in diverse organisms, including nematode worms, flies, mice and humans. Signals are initiated upon binding of TGFbeta superfamily members to cell-surface serine/thre...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Attisano L,Lee-Hoeflich ST

    更新日期:2001-01-01 00:00:00

  • The plasticity of the grapevine berry transcriptome.

    abstract:BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dal Santo S,Tornielli GB,Zenoni S,Fasoli M,Farina L,Anesi A,Guzzo F,Delledonne M,Pezzotti M

    更新日期:2013-06-07 00:00:00

  • Going beyond genetics to discover cancer targets.

    abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sandoval GJ,Hahn WC

    更新日期:2017-05-22 00:00:00

  • The first aurochs genome reveals the breeding history of British and European cattle.

    abstract::The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章


    authors: Orlando L

    更新日期:2015-10-26 00:00:00

  • Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

    abstract::Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yang S,Corbett SE,Koga Y,Wang Z,Johnson WE,Yajima M,Campbell JD

    更新日期:2020-03-05 00:00:00

  • The ribosomal protein genes and Minute loci of Drosophila melanogaster.

    abstract:BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Marygold SJ,Roote J,Reuter G,Lambertsson A,Ashburner M,Millburn GH,Harrison PM,Yu Z,Kenmochi N,Kaufman TC,Leevers SJ,Cook KR

    更新日期:2007-01-01 00:00:00

  • Wheat functional genomics and engineering crop improvement.

    abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Francki M,Appels R

    更新日期:2002-01-01 00:00:00

  • Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast.

    abstract:BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ruotolo R,Marchini G,Ottonello S

    更新日期:2008-04-07 00:00:00

  • Protein profiling comes of age.

    abstract::Ever since DNA microarrays were first applied to the quantitation of RNA levels, there has been considerable interest in generating a protein homolog that can be used to assay cellular protein expression. A recent paper describes the first microarray that can be used for such protein profiling. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Tomlinson IM,Holt LJ

    更新日期:2001-01-01 00:00:00

  • The WUS homeobox-containing (WOX) protein family.

    abstract::The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: van der Graaff E,Laux T,Rensing SA

    更新日期:2009-01-01 00:00:00

  • Games with a scientific purpose.

    abstract::The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Good BM,Su AI

    更新日期:2011-12-28 00:00:00

  • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.

    abstract:BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

    更新日期:2015-04-01 00:00:00

  • Rapid gene isolation in barley and wheat by mutant chromosome sequencing.

    abstract::Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

    更新日期:2016-10-31 00:00:00

  • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    abstract::Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

    更新日期:2012-08-31 00:00:00

  • Gene editing of the multi-copy H2A.B gene and its importance for fertility.

    abstract:BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Anuar ND,Kurscheid S,Field M,Zhang L,Rebar E,Gregory P,Buchou T,Bowles J,Koopman P,Tremethick DJ,Soboleva TA

    更新日期:2019-01-31 00:00:00

  • Epigenetic engineering and the art of epigenetic manipulation.

    abstract::A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

    journal_title:Genome biology



    authors: Magnani L

    更新日期:2014-01-01 00:00:00

  • Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages.

    abstract:BACKGROUND:It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromer...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Bulazel KV,Ferreri GC,Eldridge MD,O'Neill RJ

    更新日期:2007-01-01 00:00:00

  • Old soldiers never die ....

    abstract::An ancestral supersoldier phenotype of Pheidole ants can be recovered when selection for supersoldiers re-emerges, indicating that the developmental potential for caste pathways is retained. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Boomsma JJ,Nygaard S

    更新日期:2012-02-22 00:00:00