Surveying genome replication.


:Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized.


Genome Biol


Genome biology


Kearsey S





Has Abstract


2002-01-01 00:00:00












  • A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development.

    abstract:BACKGROUND:Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ashe A,Morgan DK,Whitelaw NC,Bruxner TJ,Vickaryous NK,Cox LL,Butterfield NC,Wicking C,Blewitt ME,Wilkins SJ,Anderson GJ,Cox TC,Whitelaw E

    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

  • Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.

    abstract:BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

    更新日期:2007-01-01 00:00:00

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

    abstract::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 insertio...

    journal_title:Genome biology

    pub_type: 杂志文章


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

    更新日期:2004-01-01 00:00:00

  • KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation.

    abstract:BACKGROUND:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. RESULTS:Here, we show that KDM5B, which demethylates lysine 4 of histone H3...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Kidder BL,Hu G,Zhao K

    更新日期:2014-02-04 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

  • Multiclass classification of microarray data with repeated measurements: application to cancer.

    abstract::Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. We have developed the uncorrelated shrunken centroid (USC) and error-weighted, uncorrelated shrunken centroid (EWUSC) algorithms...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yeung KY,Bumgarner RE

    更新日期:2003-01-01 00:00:00

  • Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.

    abstract::We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rasmussen M,Sundström M,Göransson Kultima H,Botling J,Micke P,Birgisson H,Glimelius B,Isaksson A

    更新日期:2011-10-24 00:00:00

  • The greatest catch: big game fishing for mRNA-bound proteins.

    abstract::Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...

    journal_title:Genome biology



    authors: Sibley CR,Attig J,Ule J

    更新日期:2012-07-17 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

  • Observation of intermittency in gene expression on cDNA microarrays.

    abstract::We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Peterson LE,Lau K

    更新日期:2002-05-29 00:00:00

  • Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

    abstract:BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

    更新日期:2015-04-16 00:00:00

  • Studying alternative splicing regulatory networks through partial correlation analysis.

    abstract:BACKGROUND:Alternative pre-mRNA splicing is an important gene regulation mechanism for expanding proteomic diversity in higher eukaryotes. Each splicing regulator can potentially influence a large group of alternative exons. Meanwhile, each alternative exon is controlled by multiple splicing regulators. The rapid accum...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Chen L,Zheng S

    更新日期:2009-01-01 00:00:00

  • xCell: digitally portraying the tissue cellular heterogeneity landscape.

    abstract::Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Aran D,Hu Z,Butte AJ

    更新日期:2017-11-15 00:00:00

  • Concept recognition for extracting protein interaction relations from biomedical text.

    abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

    更新日期:2008-01-01 00:00:00

  • Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression.

    abstract:BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Wu J,Xie X

    更新日期:2006-01-01 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


    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

  • Large-scale and high-confidence proteomic analysis of human seminal plasma.

    abstract:BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Pilch B,Mann M

    更新日期:2006-01-01 00:00:00

  • Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type.

    abstract:BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Franco I,Helgadottir HT,Moggio A,Larsson M,Vrtačnik P,Johansson A,Norgren N,Lundin P,Mas-Ponte D,Nordström J,Lundgren T,Stenvinkel P,Wennberg L,Supek F,Eriksson M

    更新日期:2019-12-18 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

  • RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein

    abstract:BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gibson TJ

    更新日期:2001-01-01 00:00:00

  • PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.

    abstract::The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Krakau S,Richard H,Marsico A

    更新日期:2017-12-28 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

  • Genotyping structural variants in pangenome graphs using the vg toolkit.

    abstract::Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B

    更新日期:2020-02-12 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 plasticity of the grapevine berry transcriptome.

    abstract:BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dal Santo S,Tornielli GB,Zenoni S,Fasoli M,Farina L,Anesi A,Guzzo F,Delledonne M,Pezzotti M

    更新日期:2013-06-07 00:00:00

  • Genomics through the lens of next-generation sequencing.

    abstract::A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Capra JA,Carbone L,Riesenfeld SJ,Wall JD

    更新日期:2010-01-01 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

  • 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


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

    更新日期:2006-01-01 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


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

    更新日期:2005-01-01 00:00:00