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


: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:


Genome Biol


Genome biology


Orlando L




Has Abstract


2015-10-26 00:00:00












  • Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma.

    abstract:BACKGROUND:Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosi...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gao F,Xia Y,Wang J,Lin Z,Ou Y,Liu X,Liu W,Zhou B,Luo H,Zhou B,Wen B,Zhang X,Huang J

    更新日期:2014-12-03 00:00:00

  • CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

    abstract::Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hashimshony T,Senderovich N,Avital G,Klochendler A,de Leeuw Y,Anavy L,Gennert D,Li S,Livak KJ,Rozenblatt-Rosen O,Dor Y,Regev A,Yanai I

    更新日期:2016-04-28 00:00:00

  • Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis.

    abstract:BACKGROUND:Piwi-interacting RNAs (piRNAs) are a class of short (~26-31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs). Maternal loading of piRN...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ninova M,Griffiths-Jones S,Ronshaugen M

    更新日期:2017-09-26 00:00:00

  • Fate by RNA methylation: m6A steers stem cell pluripotency.

    abstract::The N 6-methyladenosine (m6A) modification of mRNA has a crucial function in regulating pluripotency in murine stem cells: it facilitates resolution of naïve pluripotency towards differentiation. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Zhao BS,He C

    更新日期:2015-02-22 00:00:00

  • Identifying repeat domains in large genomes.

    abstract::We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zhi D,Raphael BJ,Price AL,Tang H,Pevzner PA

    更新日期:2006-01-01 00:00:00

  • Surveying genome replication.

    abstract::Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Kearsey S

    更新日期:2002-01-01 00:00:00

  • A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development.

    abstract:BACKGROUND:Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ashe A,Morgan DK,Whitelaw NC,Bruxner TJ,Vickaryous NK,Cox LL,Butterfield NC,Wicking C,Blewitt ME,Wilkins SJ,Anderson GJ,Cox TC,Whitelaw E

    更新日期:2008-01-01 00:00:00

  • Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.

    abstract:UNLABELLED:Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterati...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Renaud G,Slon V,Duggan AT,Kelso J

    更新日期:2015-10-12 00:00:00

  • Illuminating the genome-wide activity of genome editors for safe and effective therapeutics.

    abstract::Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Cheng Y,Tsai SQ

    更新日期:2018-12-22 00:00:00

  • Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.

    abstract:BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

    更新日期:2019-02-21 00:00:00

  • Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle.

    abstract:BACKGROUND:Using oligonucleotide microarrays, we compared transcriptional profiles corresponding to the initial cell cycle stages of mouse fibroblasts lacking the small GTPases H-Ras and/or N-Ras with those of matching, wild-type controls. RESULTS:Serum-starved wild-type and knockout ras fibroblasts had very similar t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Castellano E,Guerrero C,Núñez A,De Las Rivas J,Santos E

    更新日期:2009-01-01 00:00:00

  • Pigs taking wing with transposons and recombinases.

    abstract::Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Clark KJ,Carlson DF,Fahrenkrug SC

    更新日期:2007-01-01 00:00:00

  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi.

    abstract:BACKGROUND:Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Burmester A,Shelest E,Glöckner G,Heddergott C,Schindler S,Staib P,Heidel A,Felder M,Petzold A,Szafranski K,Feuermann M,Pedruzzi I,Priebe S,Groth M,Winkler R,Li W,Kniemeyer O,Schroeckh V,Hertweck C,Hube B,White TC

    更新日期:2011-01-01 00:00:00

  • The bovine lactation genome: insights into the evolution of mammalian milk.

    abstract:BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

    更新日期:2009-01-01 00:00:00

  • Networks for all.

    abstract::A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008. ...

    journal_title:Genome biology



    authors: Ahnert SE,Teichmann SA

    更新日期:2008-10-27 00:00:00

  • Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.

    abstract:BACKGROUND:Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic d...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lawson MJ,Zhang L

    更新日期:2006-01-01 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

  • iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.

    abstract::The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

    更新日期:2017-01-18 00:00:00

  • Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs.

    abstract:BACKGROUND:Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA patho...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Cervera A,Urbina D,de la Peña M

    更新日期:2016-06-23 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

  • Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.

    abstract:BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Narsai R,Gouil Q,Secco D,Srivastava A,Karpievitch YV,Liew LC,Lister R,Lewsey MG,Whelan J

    更新日期:2017-09-15 00:00:00

  • Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome.

    abstract:BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

    更新日期:2006-01-01 00:00:00

  • Statistical tests for differential expression in cDNA microarray experiments.

    abstract::Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Cui X,Churchill GA

    更新日期:2003-01-01 00:00:00

  • In silico meets in vivo.

    abstract::A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

    journal_title:Genome biology



    authors: Weng Z,Guigó R

    更新日期:2008-01-01 00:00:00

  • An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

    abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

    更新日期:2019-01-08 00:00:00

  • Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence.

    abstract:BACKGROUND:Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced follow...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Han R,Li L,Ugalde AP,Tal A,Manber Z,Barbera EP,Chiara VD,Elkon R,Agami R

    更新日期:2018-08-17 00:00:00

  • Changes in the organization of the genome during the mammalian cell cycle.

    abstract::By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Giorgetti L,Servant N,Heard E

    更新日期:2013-12-24 00:00:00

  • Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

    abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

    更新日期:2015-01-29 00:00:00

  • Multiple RNA-protein interactions in Drosophila dosage compensation.

    abstract::From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Amrein H

    更新日期:2000-01-01 00:00:00

  • Assessing taxonomic metagenome profilers with OPAL.

    abstract::The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Meyer F,Bremges A,Belmann P,Janssen S,McHardy AC,Koslicki D

    更新日期:2019-03-04 00:00:00