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: www.dx.doi.org/10.1186/s13059-015-0790-2.

journal_name

Genome Biol

journal_title

Genome biology

authors

Orlando L

doi

10.1186/s13059-015-0793-z

subject

Has Abstract

pub_date

2015-10-26 00:00:00

pages

225

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-015-0793-z

journal_volume

16

pub_type

评论,杂志文章
  • Inferring protein domain interactions from databases of interacting proteins.

    abstract::We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, Eij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In to...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-10-r89

    authors: Riley R,Lee C,Sabatti C,Eisenberg D

    更新日期:2005-01-01 00:00:00

  • The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

    abstract::We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-3-r29

    authors: Hayamizu TF,Mangan M,Corradi JP,Kadin JA,Ringwald M

    更新日期:2005-01-01 00:00:00

  • AirLab: a cloud-based platform to manage and share antibody-based single-cell research.

    abstract::Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodi...

    journal_title:Genome biology

    pub_type: 信件

    doi:10.1186/s13059-016-1006-0

    authors: Catena R,Özcan A,Jacobs A,Chevrier S,Bodenmiller B

    更新日期:2016-06-29 00:00:00

  • Molecular archeology of L1 insertions in the human genome.

    abstract:BACKGROUND:As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after in...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-10-research0052

    authors: Szak ST,Pickeral OK,Makalowski W,Boguski MS,Landsman D,Boeke JD

    更新日期:2002-09-19 00:00:00

  • Global and unbiased detection of splice junctions from RNA-seq data.

    abstract::We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2010-11-3-r34

    authors: Ameur A,Wetterbom A,Feuk L,Gyllensten U

    更新日期:2010-01-01 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

    doi:10.1186/s13059-019-1924-8

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

    更新日期:2020-01-22 00:00:00

  • Accelerating research through reagent repositories: the genome editing example.

    abstract::Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...

    journal_title:Genome biology

    pub_type: 面试

    doi:10.1186/s13059-015-0830-y

    authors: Joung JK,Voytas DF,Kamens J

    更新日期:2015-11-20 00:00:00

  • Exploiting microarrays to reveal differential gene expression in the nervous system.

    abstract::Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differen...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-2-105

    authors: Griffin RS,Mills CD,Costigan M,Woolf CJ

    更新日期:2003-01-01 00:00:00

  • Modular organization in the reductive evolution of protein-protein interaction networks.

    abstract:BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-5-r94

    authors: Tamames J,Moya A,Valencia A

    更新日期:2007-01-01 00:00:00

  • Epigenetic modifications of histones in cancer.

    abstract::The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we revie...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/s13059-019-1870-5

    authors: Zhao Z,Shilatifard A

    更新日期:2019-11-20 00:00:00

  • Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.

    abstract::A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-to-T mutations. We further profile the accessibiliti...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1839-4

    authors: Wang Y,Gao R,Wu J,Xiong YC,Wei J,Zhang S,Yang B,Chen J,Yang L

    更新日期:2019-10-23 00:00:00

  • Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders.

    abstract:BACKGROUND:Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genom...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1043-8

    authors: Uusküla-Reimand L,Hou H,Samavarchi-Tehrani P,Rudan MV,Liang M,Medina-Rivera A,Mohammed H,Schmidt D,Schwalie P,Young EJ,Reimand J,Hadjur S,Gingras AC,Wilson MD

    更新日期:2016-08-31 00:00:00

  • Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation.

    abstract:BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0476-1

    authors: Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

    更新日期:2014-01-01 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

    doi:10.1186/gb-2003-4-4-210

    authors: Cui X,Churchill GA

    更新日期:2003-01-01 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

    doi:10.1186/gb-2006-7-1-201

    authors: Kellam P

    更新日期:2006-01-01 00:00:00

  • Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.

    abstract:BACKGROUND:The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-10-r152

    authors: Satou Y,Mineta K,Ogasawara M,Sasakura Y,Shoguchi E,Ueno K,Yamada L,Matsumoto J,Wasserscheid J,Dewar K,Wiley GB,Macmil SL,Roe BA,Zeller RW,Hastings KE,Lemaire P,Lindquist E,Endo T,Hotta K,Inaba K

    更新日期:2008-10-14 00:00:00

  • Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.

    abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1848-3

    authors: Sa JK,Hwang JR,Cho YJ,Ryu JY,Choi JJ,Jeong SY,Kim J,Kim MS,Paik ES,Lee YY,Choi CH,Kim TJ,Kim BG,Bae DS,Lee Y,Her NG,Shin YJ,Cho HJ,Kim JY,Seo YJ,Koo H,Oh JW,Lee T,Kim HS,Song SY,Bae JS,Park WY,Han HD

    更新日期:2019-11-26 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

    doi:10.1186/s13059-020-1950-6

    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 first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

    abstract:BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0780-4

    authors: Chung O,Jin S,Cho YS,Lim J,Kim H,Jho S,Kim HM,Jun J,Lee H,Chon A,Ko J,Edwards J,Weber JA,Han K,O'Brien SJ,Manica A,Bhak J,Paek WK

    更新日期:2015-10-21 00:00:00

  • Quantitative reconstruction of leukocyte subsets using DNA methylation.

    abstract:BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-3-r50

    authors: Accomando WP,Wiencke JK,Houseman EA,Nelson HH,Kelsey KT

    更新日期:2014-03-05 00:00:00

  • The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.

    abstract:BACKGROUND:Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0457-4

    authors: Formey D,Sallet E,Lelandais-Brière C,Ben C,Bustos-Sanmamed P,Niebel A,Frugier F,Combier JP,Debellé F,Hartmann C,Poulain J,Gavory F,Wincker P,Roux C,Gentzbittel L,Gouzy J,Crespi M

    更新日期:2014-09-24 00:00:00

  • What does biologically meaningful mean? A perspective on gene regulatory network validation.

    abstract::Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-4-109

    authors: Walhout AJ

    更新日期:2011-01-01 00:00:00

  • A cell surface interaction network of neural leucine-rich repeat receptors.

    abstract:BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-9-r99

    authors: Söllner C,Wright GJ

    更新日期:2009-01-01 00:00:00

  • Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.

    abstract::A central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomar...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2010-11-2-r13

    authors: Fortney K,Kotlyar M,Jurisica I

    更新日期:2010-01-01 00:00:00

  • Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.

    abstract:BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1894-x

    authors: Kentepozidou E,Aitken SJ,Feig C,Stefflova K,Ibarra-Soria X,Odom DT,Roller M,Flicek P

    更新日期:2020-01-07 00:00:00

  • Predicting the effects of frameshifting indels.

    abstract::Each human has approximately 50 to 280 frameshifting indels, yet their implications are unknown. We created SIFT Indel, a prediction method for frameshifting indels that has 84% accuracy. The percentage of human frameshifting indels predicted to be gene-damaging is negatively correlated with allele frequency. We also ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2012-13-2-r9

    authors: Hu J,Ng PC

    更新日期:2012-02-09 00:00:00

  • EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

    abstract::The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-4-r39

    authors: Fischer A,Illingworth CJ,Campbell PJ,Mustonen V

    更新日期:2013-04-29 00:00:00

  • Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells.

    abstract:BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1445-x

    authors: Wang Y,Liu KI,Sutrisnoh NB,Srinivasan H,Zhang J,Li J,Zhang F,Lalith CRJ,Xing H,Shanmugam R,Foo JN,Yeo HT,Ooi KH,Bleckwehl T,Par YYR,Lee SM,Ismail NNB,Sanwari NAB,Lee STV,Lew J,Tan MH

    更新日期:2018-05-29 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

    doi:10.1186/gb-2006-7-1-r7

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

    更新日期:2006-01-01 00:00:00

  • Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

    abstract:BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0683-4

    authors: Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

    更新日期:2015-06-09 00:00:00