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




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2015-10-26 00:00:00












  • SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

    abstract::Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Jiang Y,Zhang NR,Li M

    更新日期:2017-04-26 00:00:00

  • Wheat chromatin architecture is organized in genome territories and transcription factories.

    abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Concia L,Veluchamy A,Ramirez-Prado JS,Martin-Ramirez A,Huang Y,Perez M,Domenichini S,Rodriguez Granados NY,Kim S,Blein T,Duncan S,Pichot C,Manza-Mianza D,Juery C,Paux E,Moore G,Hirt H,Bergounioux C,Crespi M,Mahfouz

    更新日期:2020-04-29 00:00:00

  • Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.

    abstract:BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Xie G,Bonner CA,Jensen RA

    更新日期:2002-08-29 00:00:00

  • Opening sequence: computational genomics in the era of high-throughput sequencing.

    abstract::A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

    journal_title:Genome biology



    authors: Chambers EV,Kindt AS,Semple CA

    更新日期:2011-12-28 00:00:00

  • Methylome evolution in plants.

    abstract::Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is l...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Vidalis A,Živković D,Wardenaar R,Roquis D,Tellier A,Johannes F

    更新日期:2016-12-20 00:00:00

  • Avianbase: a community resource for bird genomics.

    abstract::Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

    journal_title:Genome biology

    pub_type: 信件


    authors: Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

    更新日期:2015-01-29 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

  • A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.

    abstract:BACKGROUND:Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species....

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hane JK,Rouxel T,Howlett BJ,Kema GH,Goodwin SB,Oliver RP

    更新日期:2011-01-01 00:00:00

  • Having a BLAST with bioinformatics (and avoiding BLASTphemy).

    abstract::Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the princi...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Pertsemlidis A,Fondon JW 3rd

    更新日期:2001-01-01 00:00:00

  • Responses of hyperthermophilic crenarchaea to UV irradiation.

    abstract:BACKGROUND:DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. RESUL...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Götz D,Paytubi S,Munro S,Lundgren M,Bernander R,White MF

    更新日期:2007-01-01 00:00:00

  • Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23.

    abstract:BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

    更新日期:2016-11-01 00:00:00

  • Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors.

    abstract:BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

    更新日期:2006-01-01 00:00:00

  • Attacking pathogens through their hosts.

    abstract::Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions. This new antimicrobial strategy has proved effective in the laboratory and in the clinic, and it has great potential for the futu...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Kellam P

    更新日期:2006-01-01 00:00:00

  • Organizing knowledge to enable personalization of medicine in cancer.

    abstract::Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Good BM,Ainscough BJ,McMichael JF,Su AI,Griffith OL

    更新日期:2014-08-27 00:00:00

  • Single-cell profiling of lncRNAs in the developing human brain.

    abstract::Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章


    authors: Ma Q,Chang HY

    更新日期:2016-04-14 00:00:00

  • SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds.

    abstract::We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Li C,Zong Y,Jin S,Zhu H,Lin D,Li S,Qiu JL,Wang Y,Gao C

    更新日期:2020-06-16 00:00:00

  • Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs.

    abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Wang C,Lin H

    更新日期:2021-01-08 00:00:00

  • Muscular expressions: profiling genes in complex tissues.

    abstract::Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Hampson R,Hughes SM

    更新日期:2001-01-01 00:00:00

  • A comparison of programmed cell death between species.

    abstract::Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Tittel JN,Steller H

    更新日期:2000-01-01 00:00:00

  • Mapping-by-sequencing accelerates forward genetics in barley.

    abstract::Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mascher M,Jost M,Kuon JE,Himmelbach A,Aßfalg A,Beier S,Scholz U,Graner A,Stein N

    更新日期:2014-06-10 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

  • 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

  • Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

    abstract::Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fan X,Zhang X,Wu X,Guo H,Hu Y,Tang F,Huang Y

    更新日期:2015-07-23 00:00:00

  • The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex.

    abstract:BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Verduci L,Ferraiuolo M,Sacconi A,Ganci F,Vitale J,Colombo T,Paci P,Strano S,Macino G,Rajewsky N,Blandino G

    更新日期:2017-12-20 00:00:00

  • Molecular mechanisms of spindle function.

    abstract::The key molecules involved in regulating the assembly and function of the mitotic spindle are shared by evolutionarily divergent species. Studies in different model systems are leading to convergent conclusions about the central role of microtubule nucleation and dynamics and of kinesin-related motor proteins in spind...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Walczak CE

    更新日期:2000-01-01 00:00:00

  • Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment.

    abstract:BACKGROUND:To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analy...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Suzuki A,Matsushima K,Makinoshima H,Sugano S,Kohno T,Tsuchihara K,Suzuki Y

    更新日期:2015-04-03 00:00:00

  • Expanded identification and characterization of mammalian circular RNAs.

    abstract:BACKGROUND:The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood. RESULTS:We developed a computational pipeline to ide...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Guo JU,Agarwal V,Guo H,Bartel DP

    更新日期:2014-07-29 00:00:00

  • MOABS: model based analysis of bisulfite sequencing data.

    abstract::Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Bino...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sun D,Xi Y,Rodriguez B,Park HJ,Tong P,Meong M,Goodell MA,Li W

    更新日期:2014-02-24 00:00:00

  • Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes.

    abstract:BACKGROUND:RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Bou Sleiman M,Frochaux MV,Andreani T,Osman D,Guigo R,Deplancke B

    更新日期:2020-01-17 00:00:00

  • Conserved rules govern genetic interaction degree across species.

    abstract:BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

    更新日期:2012-07-02 00:00:00