Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA.

abstract：BACKGROUND:Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like rece...

journal_title：Genome biology

authors： Wells CA,Chalk AM,Forrest A,Taylor D,Waddell N,Schroder K,Himes SR,Faulkner G,Lo S,Kasukawa T,Kawaji H,Kai C,Kawai J,Katayama S,Carninci P,Hayashizaki Y,Hume DA,Grimmond SM

更新日期：2006-01-01 00:00:00

abstract：:Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...

journal_title：Genome biology

authors： Staiger D,Shin J,Johansson M,Davis SJ

更新日期：2013-06-24 00:00:00

abstract：BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...

journal_title：Genome biology

authors： Zuccolo A,Bowers JE,Estill JC,Xiong Z,Luo M,Sebastian A,Goicoechea JL,Collura K,Yu Y,Jiao Y,Duarte J,Tang H,Ayyampalayam S,Rounsley S,Kudrna D,Paterson AH,Pires JC,Chanderbali A,Soltis DE,Chamala S,Barbazuk B,So

更新日期：2011-01-01 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：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 00:00:00

abstract：:The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...

journal_title：Genome biology

authors： Eakin GS,Hadjantonakis AK

更新日期：2006-01-01 00:00:00

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

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

abstract：:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...

journal_title：Genome biology

authors： Beeravolu CR,Hickerson MJ,Frantz LAF,Lohse K

更新日期：2018-09-25 00:00:00

abstract：:Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...

journal_title：Genome biology

authors： Jiang Y,Zhang NR,Li M

更新日期：2017-04-26 00:00:00

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

authors： Moses AM,Hériché JK,Durbin R

更新日期：2007-01-01 00:00:00

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

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

abstract：BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...

journal_title：Genome biology

authors： Tripoli G,D'Elia D,Barsanti P,Caggese C

更新日期：2005-01-01 00:00:00

abstract：:A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

journal_title：Genome biology

authors： Magnani L

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

journal_title：Genome biology

authors： Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...

journal_title：Genome biology

authors： Söllner C,Wright GJ

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

journal_title：Genome biology

authors： Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

更新日期：2013-11-22 00:00:00

abstract：BACKGROUND:Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there...

journal_title：Genome biology

authors： Ying H,Cooke I,Sprungala S,Wang W,Hayward DC,Tang Y,Huttley G,Ball EE,Forêt S,Miller DJ

更新日期：2018-11-02 00:00:00

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 00:00:00

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

authors： Conway EM,Carmeliet P

更新日期：2004-01-01 00:00:00

abstract：:How the mechanisms of dosage compensation distinguish the sex chromosomes from the autosomes has been something of a mystery. A recent study in Caenorhabditis elegans has identified clusters of two common DNA motifs as a cis-acting code for the recruitment of the DCC, the protein complex that mediates dosage compensat...

journal_title：Genome biology

authors： Deng X,Disteche CM

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

journal_title：Genome biology

authors： McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

更新日期：2016-11-01 00:00:00

abstract：BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to deve...

journal_title：Genome biology

authors： McCartney DL,Hillary RF,Stevenson AJ,Ritchie SJ,Walker RM,Zhang Q,Morris SW,Bermingham ML,Campbell A,Murray AD,Whalley HC,Gale CR,Porteous DJ,Haley CS,McRae AF,Wray NR,Visscher PM,McIntosh AM,Evans KL,Deary IJ,Mar

更新日期：2018-09-27 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：BACKGROUND:Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or activ...

journal_title：Genome biology

authors： Sidaway-Lee K,Costa MJ,Rand DA,Finkenstadt B,Penfield S

更新日期：2014-03-03 00:00:00

abstract：:Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of different...

journal_title：Genome biology

authors： Li Y,Yang H,Zhang H,Liu Y,Shang H,Zhao H,Zhang T,Tu Q

更新日期：2020-03-23 00:00:00

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

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

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

authors： Pilch B,Mann M

更新日期：2006-01-01 00:00:00

abstract：:DNA shuffling has proven to be a powerful technique for the directed evolution of proteins. A mix of theoretical and applied research has now provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions. ...

journal_title：Genome biology

authors： Bacher JM,Reiss BD,Ellington AD

更新日期：2002-07-31 00:00:00

abstract：:The N 6-methyladenosine (m6A) modification of mRNA has a crucial function in regulating pluripotency in murine stem cells: it facilitates resolution of naïve pluripotency towards differentiation. ...

journal_title：Genome biology

authors： Zhao BS,He C

更新日期：2015-02-22 00:00:00

abstract：BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

journal_title：Genome biology

authors： Xie G,Bonner CA,Jensen RA

更新日期：2002-08-29 00:00:00