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












  • 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

  • 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

  • A CRISPR design for next-generation antimicrobials.

    abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章


    authors: Beisel CL,Gomaa AA,Barrangou R

    更新日期:2014-11-08 00:00:00

  • Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.

    abstract:BACKGROUND:Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS:We use high throughput single-cell RNA-seq...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Han X,Chen H,Huang D,Chen H,Fei L,Cheng C,Huang H,Yuan GC,Guo G

    更新日期:2018-04-05 00:00:00

  • MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.

    abstract::We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show tha...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zhu Z,Ren J,Michail S,Sun F

    更新日期:2019-08-06 00:00:00

  • Asymmetric relationships between proteins shape genome evolution.

    abstract:BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Notebaart RA,Kensche PR,Huynen MA,Dutilh BE

    更新日期:2009-02-12 00:00:00

  • Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.

    abstract::Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Zinzen RP,Furlong EE

    更新日期:2008-01-01 00:00:00

  • Dynamic systems.

    abstract::A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

    journal_title:Genome biology



    authors: Bakal C

    更新日期:2012-01-30 00:00:00

  • Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction.

    abstract:BACKGROUND:Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS:We presen...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fuxelius HH,Darby AC,Cho NH,Andersson SG

    更新日期:2008-01-01 00:00:00

  • Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

    abstract:BACKGROUND:The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Cheung WA,Shao X,Morin A,Siroux V,Kwan T,Ge B,Aïssi D,Chen L,Vasquez L,Allum F,Guénard F,Bouzigon E,Simon MM,Boulier E,Redensek A,Watt S,Datta A,Clarke L,Flicek P,Mead D,Paul DS,Beck S,Bourque G,Lathrop M,

    更新日期:2017-03-10 00:00:00

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

    abstract::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 ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Massingham T,Goldman N

    更新日期:2012-02-29 00:00:00

  • The amazing world of bacterial structured RNAs.

    abstract::The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Westhof E

    更新日期:2010-01-01 00:00:00

  • Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis.

    abstract:BACKGROUND:DNA methylation plays an essential role in regulating gene expression under a variety of conditions and it has therefore been hypothesized to underlie the transitions between life cycle stages in parasitic nematodes. So far, however, 5'-cytosine methylation has not been detected during any developmental stag...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gao F,Liu X,Wu XP,Wang XL,Gong D,Lu H,Xia Y,Song Y,Wang J,Du J,Liu S,Han X,Tang Y,Yang H,Jin Q,Zhang X,Liu M

    更新日期:2012-10-17 00:00:00

  • Using orthologous and paralogous proteins to identify specificity determining residues.

    abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mirny LA,Gelfand MS

    更新日期:2002-01-01 00:00:00

  • SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.

    abstract::Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Davidson NM,Hawkins ADK,Oshlack A

    更新日期:2017-08-04 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

  • Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.

    abstract::Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Kilpinen S,Autio R,Ojala K,Iljin K,Bucher E,Sara H,Pisto T,Saarela M,Skotheim RI,Björkman M,Mpindi JP,Haapa-Paananen S,Vainio P,Edgren H,Wolf M,Astola J,Nees M,Hautaniemi S,Kallioniemi O

    更新日期:2008-01-01 00:00:00

  • Prediction of synergistic transcription factors by function conservation.

    abstract:BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hu Z,Hu B,Collins JF

    更新日期:2007-01-01 00:00:00

  • Design and computational analysis of single-cell RNA-sequencing experiments.

    abstract::Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Bacher R,Kendziorski C

    更新日期:2016-04-07 00:00:00

  • Reduced intrinsic DNA curvature leads to increased mutation rate.

    abstract:BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

    更新日期:2018-09-14 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

  • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.

    abstract:BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Conrad TM,Joyce AR,Applebee MK,Barrett CL,Xie B,Gao Y,Palsson BØ

    更新日期:2009-01-01 00:00:00

  • The Amborella genome: an evolutionary reference for plant biology.

    abstract::The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. ...

    journal_title:Genome biology

    pub_type: 信件


    authors: Soltis DE,Albert VA,Leebens-Mack J,Palmer JD,Wing RA,dePamphilis CW,Ma H,Carlson JE,Altman N,Kim S,Wall PK,Zuccolo A,Soltis PS

    更新日期:2008-01-01 00:00:00

  • Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray.

    abstract::The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Carter MG,Sharov AA,VanBuren V,Dudekula DB,Carmack CE,Nelson C,Ko MS

    更新日期:2005-01-01 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

  • Where is genomics going next?

    abstract::We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. ...

    journal_title:Genome biology

    pub_type: 社论,面试


    authors: Cheifet B

    更新日期:2019-01-22 00:00:00

  • Chemical genomics in yeast.

    abstract::Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Brenner C

    更新日期:2004-01-01 00:00:00

  • Systematic identification of genetic influences on methylation across the human life course.

    abstract:BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

    更新日期:2016-03-31 00:00:00

  • Emerging roles of chromatin in the maintenance of genome organization and function in plants.

    abstract::Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Vergara Z,Gutierrez C

    更新日期:2017-05-23 00:00:00

  • Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).

    abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yao Y,Guo G,Ni Z,Sunkar R,Du J,Zhu JK,Sun Q

    更新日期:2007-01-01 00:00:00