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

abstract：BACKGROUND:The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it r...

journal_title：Genome biology

authors： Pietzenuk B,Markus C,Gaubert H,Bagwan N,Merotto A,Bucher E,Pecinka A

更新日期：2016-10-11 00:00:00

abstract：BACKGROUND:Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolut...

journal_title：Genome biology

authors： Kondrashov FA,Rogozin IB,Wolf YI,Koonin EV

更新日期：2002-01-01 00:00:00

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

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

abstract：BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...

journal_title：Genome biology

authors： Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RA

更新日期：2008-01-01 00:00:00

abstract：:A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

journal_title：Genome biology

authors： Le Caignec C,Redon R

更新日期：2009-01-01 00:00:00

abstract：:The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

journal_title：Genome biology

authors： Good BM,Su AI

更新日期：2011-12-28 00:00:00

abstract：:MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

journal_title：Genome biology

authors： Menor M,Ching T,Zhu X,Garmire D,Garmire LX

更新日期：2014-01-01 00:00:00

abstract：:Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...

journal_title：Genome biology

authors： Good BM,Ainscough BJ,McMichael JF,Su AI,Griffith OL

更新日期：2014-08-27 00:00:00

abstract：BACKGROUND:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities,...

journal_title：Genome biology

authors： Tarallo R,Giurato G,Bruno G,Ravo M,Rizzo F,Salvati A,Ricciardi L,Marchese G,Cordella A,Rocco T,Gigantino V,Pierri B,Cimmino G,Milanesi L,Ambrosino C,Nyman TA,Nassa G,Weisz A

更新日期：2017-10-06 00:00:00

abstract：BACKGROUND:ADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected b...

journal_title：Genome biology

authors： Pinto Y,Cohen HY,Levanon EY

更新日期：2014-01-07 00:00:00

abstract：BACKGROUND:Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functio...

journal_title：Genome biology

authors： Cloonan N,Wani S,Xu Q,Gu J,Lea K,Heater S,Barbacioru C,Steptoe AL,Martin HC,Nourbakhsh E,Krishnan K,Gardiner B,Wang X,Nones K,Steen JA,Matigian NA,Wood DL,Kassahn KS,Waddell N,Shepherd J,Lee C,Ichikawa J,McKer

更新日期：2011-12-30 00:00:00

abstract：:We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...

journal_title：Genome biology

authors： Fang J,Ma Q,Chu C,Huang B,Li L,Cai P,Batista PJ,Tolentino KEM,Xu J,Li R,Du P,Qu K,Chang HY

更新日期：2019-12-20 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...

journal_title：Genome biology

authors： Wicker T,Gundlach H,Spannagl M,Uauy C,Borrill P,Ramírez-González RH,De Oliveira R,International Wheat Genome Sequencing Consortium.,Mayer KFX,Paux E,Choulet F

更新日期：2018-08-17 00:00:00

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

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

abstract：:Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...

journal_title：Genome biology

authors： Haber M,Mezzavilla M,Xue Y,Tyler-Smith C

更新日期：2016-01-11 00:00:00

abstract：BACKGROUND:Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consistin...

journal_title：Genome biology

authors： Brochier C,Forterre P,Gribaldo S

更新日期：2004-01-01 00:00:00

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

authors： Mirny LA,Gelfand MS

更新日期：2002-01-01 00:00:00

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

authors： Chen L,Zheng S

更新日期：2009-01-01 00:00:00

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

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

abstract：BACKGROUND:Gene duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...

journal_title：Genome biology

authors： Díaz-Mejía JJ,Pérez-Rueda E,Segovia L

更新日期：2007-01-01 00:00:00

abstract：:An ancestral supersoldier phenotype of Pheidole ants can be recovered when selection for supersoldiers re-emerges, indicating that the developmental potential for caste pathways is retained. ...

journal_title：Genome biology

authors： Boomsma JJ,Nygaard S

更新日期：2012-02-22 00:00:00

abstract：:Epithelial tissues house gammadelta T cells, which are important for the mucosal immune system and may be involved in controlling malignancies, infections and inflammation. Whole-genome gene-expression analysis provides a new way to study the signals required for the activation of gammadelta T cells, their mode of act...

journal_title：Genome biology

authors： Boismenu R,Havran WL

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...

journal_title：Genome biology

authors： Bourguet P,López-González L,Gómez-Zambrano Á,Pélissier T,Hesketh A,Potok ME,Pouch-Pélissier MN,Perez M,Da Ines O,Latrasse D,White CI,Jacobsen SE,Benhamed M,Mathieu O

更新日期：2020-11-25 00:00:00

abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

journal_title：Genome biology

authors： Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

更新日期：2006-01-01 00:00:00

abstract：:We demonstrate that loss-of-function yeast phenotypes are predictable by guilt-by-association in functional gene networks. Testing 1,102 loss-of-function phenotypes from genome-wide assays of yeast reveals predictability of diverse phenotypes, spanning cellular morphology, growth, metabolism, and quantitative cell sha...

journal_title：Genome biology

authors： McGary KL,Lee I,Marcotte EM

更新日期：2007-01-01 00:00:00

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

authors： Davidson NM,Hawkins ADK,Oshlack A

更新日期：2017-08-04 00:00:00

abstract：BACKGROUND:Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically p...

journal_title：Genome biology

authors： Chen R,Morgan AA,Dudley J,Deshpande T,Li L,Kodama K,Chiang AP,Butte AJ

更新日期：2008-01-01 00:00:00

abstract：SUMMARY:The large transforming growth factor-beta (TGFbeta) superfamily of secreted proteins regulate the growth, development and differentiation of cells in diverse organisms, including nematode worms, flies, mice and humans. Signals are initiated upon binding of TGFbeta superfamily members to cell-surface serine/thre...

journal_title：Genome biology

authors： Attisano L,Lee-Hoeflich ST

更新日期：2001-01-01 00:00:00

abstract：:We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological O...

journal_title：Genome biology

authors： Bard J,Rhee SY,Ashburner M

更新日期：2005-01-01 00:00:00

abstract：:DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....

journal_title：Genome biology

authors： Lausted C,Dahl T,Warren C,King K,Smith K,Johnson M,Saleem R,Aitchison J,Hood L,Lasky SR

更新日期：2004-01-01 00:00:00