Genome-wide mutagenesis of Zea mays L. using RescueMu transposons.


:Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants.


Genome Biol


Genome biology


Fernandes J,Dong Q,Schneider B,Morrow DJ,Nan GL,Brendel V,Walbot V





Has Abstract


2004-01-01 00:00:00














  • A fuzzy gene expression-based computational approach improves breast cancer prognostication.

    abstract::Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

    更新日期:2010-01-01 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

  • Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.

    abstract:BACKGROUND:Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level. RESULTS:To provide an inter-tissue view of obesity with respec...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dobrin R,Zhu J,Molony C,Argman C,Parrish ML,Carlson S,Allan MF,Pomp D,Schadt EE

    更新日期:2009-01-01 00:00:00

  • Personalized and graph genomes reveal missing signal in epigenomic data.

    abstract:BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Groza C,Kwan T,Soranzo N,Pastinen T,Bourque G

    更新日期:2020-05-25 00:00:00

  • Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences.

    abstract:BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

    更新日期:2014-06-30 00:00:00

  • Statistical tools for synthesizing lists of differentially expressed features in related experiments.

    abstract::We propose a novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio. We present a Bayesian analysis of this ratio, which leads us to suggest two rules for choosing a cut-off on the ranked list of p ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Blangiardo M,Richardson S

    更新日期:2007-01-01 00:00:00

  • New tricks for old NODs.

    abstract::Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Pietras EM,Cheng G

    更新日期:2008-04-25 00:00:00

  • Variations in abundance: genome-wide responses to genetic variation and vice versa.

    abstract::How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approa...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Hamilton BA

    更新日期:2002-09-19 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

  • Immunostaining of modified histones defines high-level features of the human metaphase epigenome.

    abstract:BACKGROUND:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Terrenoire E,McRonald F,Halsall JA,Page P,Illingworth RS,Taylor AM,Davison V,O'Neill LP,Turner BM

    更新日期:2010-01-01 00:00:00

  • Characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

    abstract:BACKGROUND:High-density oligonucleotide microarrays provide a powerful tool for assessing differential mRNA expression levels. Characterizing the noise resulting from the enzymatic and hybridization steps, called type I noise, is essential for attributing significance measures to the differential expression scores. We ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Naef F,Hacker CR,Patil N,Magnasco M

    更新日期:2002-01-01 00:00:00

  • Wheat functional genomics and engineering crop improvement.

    abstract::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 agronom...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Francki M,Appels R

    更新日期:2002-01-01 00:00:00

  • Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map.

    abstract:BACKGROUND:Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypano...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Cooper A,Tait A,Sweeney L,Tweedie A,Morrison L,Turner CM,MacLeod A

    更新日期:2008-01-01 00:00:00

  • Large scale genomic reorganization of topological domains at the HoxD locus.

    abstract:BACKGROUND:The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements lo...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fabre PJ,Leleu M,Mormann BH,Lopez-Delisle L,Noordermeer D,Beccari L,Duboule D

    更新日期:2017-08-07 00:00:00

  • Accurate and equitable medical genomic analysis requires an understanding of demography and its influence on sample size and ratio.

    abstract::In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...

    journal_title:Genome biology

    pub_type: 评论,信件


    authors: Kessler MD,O'Connor TD

    更新日期:2017-02-27 00:00:00

  • The real cost of sequencing: scaling computation to keep pace with data generation.

    abstract::As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Muir P,Li S,Lou S,Wang D,Spakowicz DJ,Salichos L,Zhang J,Weinstock GM,Isaacs F,Rozowsky J,Gerstein M

    更新日期:2016-03-23 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

  • Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis.

    abstract:BACKGROUND:Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential rol...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Heraud-Farlow JE,Chalk AM,Linder SE,Li Q,Taylor S,White JM,Pang L,Liddicoat BJ,Gupte A,Li JB,Walkley CR

    更新日期:2017-09-05 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

  • 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

  • Functions, structure, and read-through alternative splicing of feline APOBEC3 genes.

    abstract:BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Münk C,Beck T,Zielonka J,Hotz-Wagenblatt A,Chareza S,Battenberg M,Thielebein J,Cichutek K,Bravo IG,O'Brien SJ,Löchelt M,Yuhki N

    更新日期:2008-01-01 00:00:00

  • Consensus clustering and functional interpretation of gene-expression data.

    abstract::Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Swift S,Tucker A,Vinciotti V,Martin N,Orengo C,Liu X,Kellam P

    更新日期:2004-01-01 00:00:00

  • The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci.

    abstract:BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

    更新日期:2017-05-31 00:00:00

  • Identification of transcription factor binding sites using ATAC-seq.

    abstract::Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Li Z,Schulz MH,Look T,Begemann M,Zenke M,Costa IG

    更新日期:2019-02-26 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

  • 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

  • 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

  • Alternative splicing is required for stage differentiation in malaria parasites.

    abstract:BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

    更新日期:2019-08-01 00:00:00

  • Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

    abstract:BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 ben...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lim EL,Trinh DL,Scott DW,Chu A,Krzywinski M,Zhao Y,Robertson AG,Mungall AJ,Schein J,Boyle M,Mottok A,Ennishi D,Johnson NA,Steidl C,Connors JM,Morin RD,Gascoyne RD,Marra MA

    更新日期:2015-01-29 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


    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