Wheat functional genomics and engineering crop improvement.


: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 agronomically important traits.


Genome Biol


Genome biology


Francki M,Appels R





Has Abstract


2002-01-01 00:00:00












  • The cryptochromes.

    abstract::Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Lin C,Todo T

    更新日期:2005-01-01 00:00:00

  • Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans.

    abstract:BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Katju V,Farslow JC,Bergthorsson U

    更新日期:2009-01-01 00:00:00

  • Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum.

    abstract:BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

    更新日期:2013-11-22 00:00:00

  • Domain atrophy creates rare cases of functional partial protein domains.

    abstract:BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Prakash A,Bateman A

    更新日期:2015-04-30 00:00:00

  • Escape from X inactivation in mice and humans.

    abstract::A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Berletch JB,Yang F,Disteche CM

    更新日期:2010-01-01 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

  • Vertebrate gene finding from multiple-species alignments using a two-level strategy.

    abstract:BACKGROUND:One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved. RESULTS:We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separate...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Carter D,Durbin R

    更新日期:2006-01-01 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


    authors: Walhout AJ

    更新日期:2011-01-01 00:00:00

  • Improved reference genome of the arboviral vector Aedes albopictus.

    abstract:BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

    更新日期:2020-08-26 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

  • 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

  • SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.

    abstract:BACKGROUND:Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of patho...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gihawi A,Rallapalli G,Hurst R,Cooper CS,Leggett RM,Brewer DS

    更新日期:2019-10-22 00:00:00

  • Transposable elements in the mammalian embryo: pioneers surviving through stealth and service.

    abstract::Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Gerdes P,Richardson SR,Mager DL,Faulkner GJ

    更新日期:2016-05-09 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

  • The evolution of relapse of adult T cell acute lymphoblastic leukemia.

    abstract:BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sentís I,Gonzalez S,Genescà E,García-Hernández V,Muiños F,Gonzalez C,López-Arribillaga E,Gonzalez J,Fernandez-Ibarrondo L,Mularoni L,Espinosa L,Bellosillo B,Ribera JM,Bigas A,Gonzalez-Perez A,Lopez-Bigas N

    更新日期:2020-11-23 00:00:00

  • Characterization of background noise in capture-based targeted sequencing data.

    abstract:BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

    更新日期:2017-07-21 00:00:00

  • Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features.

    abstract:BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yu G,Gail MH,Consonni D,Carugno M,Humphrys M,Pesatori AC,Caporaso NE,Goedert JJ,Ravel J,Landi MT

    更新日期:2016-07-28 00:00:00

  • An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes.

    abstract:BACKGROUND:Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ghaffari S,Hanson C,Schmidt RE,Bouchonville KJ,Offer SM,Sinha S

    更新日期:2021-01-07 00:00:00

  • AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.

    abstract::Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Shahryary Y,Symeonidi A,Hazarika RR,Denkena J,Mubeen T,Hofmeister B,van Gurp T,Colomé-Tatché M,Verhoeven KJF,Tuskan G,Schmitz RJ,Johannes F

    更新日期:2020-10-06 00:00:00

  • DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.

    abstract:BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rosenthal R,McGranahan N,Herrero J,Taylor BS,Swanton C

    更新日期:2016-02-22 00:00:00

  • Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.

    abstract:BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

    更新日期:2011-10-17 00:00:00

  • Localizing the proteome.

    abstract::The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Simpson JC,Pepperkok R

    更新日期:2003-01-01 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

  • Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps.

    abstract:BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

    更新日期:2008-01-01 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

  • Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex.

    abstract:BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Liu Z,Ran Y,Tao C,Li S,Chen J,Yang E

    更新日期:2019-05-20 00:00:00

  • Anticipating the 1,000 dollar genome.

    abstract::A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diag...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mardis ER

    更新日期:2006-01-01 00:00:00

  • EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

    abstract::Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells fro...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lun ATL,Riesenfeld S,Andrews T,Dao TP,Gomes T,participants in the 1st Human Cell Atlas Jamboree.,Marioni JC

    更新日期:2019-03-22 00:00:00

  • Benchmarking of computational error-correction methods for next-generation sequencing data.

    abstract:BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

    更新日期:2020-03-17 00:00:00

  • The real cost of sequencing: higher than you think!

    abstract::Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sboner A,Mu XJ,Greenbaum D,Auerbach RK,Gerstein MB

    更新日期:2011-08-25 00:00:00