Homologous recombination: from model organisms to human disease.


:Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis.


Genome Biol


Genome biology


Modesti M,Kanaar R





Has Abstract


2001-01-01 00:00:00












  • Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling.

    abstract:BACKGROUND:Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. RESULTS:We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood c...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zannas AS,Arloth J,Carrillo-Roa T,Iurato S,Röh S,Ressler KJ,Nemeroff CB,Smith AK,Bradley B,Heim C,Menke A,Lange JF,Brückl T,Ising M,Wray NR,Erhardt A,Binder EB,Mehta D

    更新日期:2015-12-17 00:00:00

  • Leaf senescence--not just a 'wear and tear' phenomenon.

    abstract::A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex, reflecting the activation of more than 2,000 genes in Arabidopsis, with gene products involved in a broad spectrum of regulatory, biochemical and cellular events. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Gepstein S

    更新日期:2004-01-01 00:00:00

  • Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

    abstract::Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Moses AM,Hériché JK,Durbin R

    更新日期:2007-01-01 00:00:00

  • Organizing knowledge to enable personalization of medicine in cancer.

    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

    pub_type: 杂志文章


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

    更新日期:2014-08-27 00:00:00

  • CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.

    abstract::Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Daley TP,Lin Z,Lin X,Liu Y,Wong WH,Qi LS

    更新日期:2018-10-08 00:00:00

  • Large-scale assignment of orthology: back to phylogenetics?

    abstract::Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Gabaldón T

    更新日期:2008-10-30 00:00:00

  • Modeling double strand break susceptibility to interrogate structural variation in cancer.

    abstract:BACKGROUND:Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). RESULTS:We used experimentally quantif...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ballinger TJ,Bouwman BAM,Mirzazadeh R,Garnerone S,Crosetto N,Semple CA

    更新日期:2019-02-08 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

  • Functional and regulatory profiling of energy metabolism in fission yeast.

    abstract:BACKGROUND:The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Malecki M,Bitton DA,Rodríguez-López M,Rallis C,Calavia NG,Smith GC,Bähler J

    更新日期:2016-11-25 00:00:00

  • Sequence-based genomics.

    abstract::A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002. ...

    journal_title:Genome biology



    authors: Simpson AJ

    更新日期:2002-08-27 00:00:00

  • Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris.

    abstract:BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: He YQ,Zhang L,Jiang BL,Zhang ZC,Xu RQ,Tang DJ,Qin J,Jiang W,Zhang X,Liao J,Cao JR,Zhang SS,Wei ML,Liang XX,Lu GT,Feng JX,Chen B,Cheng J,Tang JL

    更新日期:2007-01-01 00:00:00

  • Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements.

    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

    pub_type: 杂志文章


    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

  • Wrangling for microRNAs provokes much crosstalk.

    abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Marques AC,Tan J,Ponting CP

    更新日期:2011-11-21 00:00:00

  • Functional analysis of transcription factor binding sites in human promoters.

    abstract:BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Whitfield TW,Wang J,Collins PJ,Partridge EC,Aldred SF,Trinklein ND,Myers RM,Weng Z

    更新日期:2012-09-26 00:00:00

  • Gene expression analysis of nuclear factor I-A deficient mice indicates delayed brain maturation.

    abstract:BACKGROUND:Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS:To identify pot...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Wong YW,Schulze C,Streichert T,Gronostajski RM,Schachner M,Tilling T

    更新日期:2007-01-01 00:00:00

  • Barley landraces are characterized by geographically heterogeneous genomic origins.

    abstract:BACKGROUND:The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of mult...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Poets AM,Fang Z,Clegg MT,Morrell PL

    更新日期:2015-08-21 00:00:00

  • Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates.

    abstract:BACKGROUND:Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first com...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Ohshima K,Hattori M,Yada T,Gojobori T,Sakaki Y,Okada N

    更新日期:2003-01-01 00:00:00

  • Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts.

    abstract:BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mekouar M,Blanc-Lenfle I,Ozanne C,Da Silva C,Cruaud C,Wincker P,Gaillardin C,Neuvéglise C

    更新日期:2010-01-01 00:00:00

  • Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

    abstract:BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Shevchenko A,Roguev A,Schaft D,Buchanan L,Habermann B,Sakalar C,Thomas H,Krogan NJ,Shevchenko A,Stewart AF

    更新日期:2008-01-01 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

  • Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites.

    abstract:BACKGROUND:Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied m...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Harcus YM,Parkinson J,Fernández C,Daub J,Selkirk ME,Blaxter ML,Maizels RM

    更新日期:2004-01-01 00:00:00

  • The diversity of endothelial cells: a challenge for therapeutic angiogenesis.

    abstract::Vascular endothelia comprise a diverse population of cells that specialize in response to genetic programs and environmental cues to take on distinct roles in different vessels, tissues, and organs, and in response to pathophysiological stresses. Characterization of endothelial-cell diversity will facilitate the devel...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Conway EM,Carmeliet P

    更新日期:2004-01-01 00:00:00

  • An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

    abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

    更新日期:2019-01-08 00:00:00

  • Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum.

    abstract:BACKGROUND:The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistanc...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dharia NV,Sidhu AB,Cassera MB,Westenberger SJ,Bopp SE,Eastman RT,Plouffe D,Batalov S,Park DJ,Volkman SK,Wirth DF,Zhou Y,Fidock DA,Winzeler EA

    更新日期:2009-02-13 00:00:00

  • Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.

    abstract:BACKGROUND:Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic d...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lawson MJ,Zhang L

    更新日期:2006-01-01 00:00:00

  • Old soldiers never die ....

    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

    pub_type: 杂志文章


    authors: Boomsma JJ,Nygaard S

    更新日期:2012-02-22 00:00:00

  • Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    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

    pub_type: 历史文章,杂志文章,评审


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

    更新日期:2016-01-11 00:00:00

  • Butterfly gene flow goes berserk.

    abstract::A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章


    authors: Ffrench-Constant RH

    更新日期:2016-02-27 00:00:00

  • Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains.

    abstract:BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Rohmer L,Fong C,Abmayr S,Wasnick M,Larson Freeman TJ,Radey M,Guina T,Svensson K,Hayden HS,Jacobs M,Gallagher LA,Manoil C,Ernst RK,Drees B,Buckley D,Haugen E,Bovee D,Zhou Y,Chang J,Levy R,Lim R,Gillett W,Guenth

    更新日期:2007-01-01 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