Muscular expressions: profiling genes in complex tissues.

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：BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

journal_title：Genome biology

authors： Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

更新日期：2007-01-01 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：:Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

journal_title：Genome biology

authors： Walhout AJ

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...

journal_title：Genome biology

authors： Anuar ND,Kurscheid S,Field M,Zhang L,Rebar E,Gregory P,Buchou T,Bowles J,Koopman P,Tremethick DJ,Soboleva TA

更新日期：2019-01-31 00:00:00

abstract：BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

journal_title：Genome biology

authors： Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

更新日期：2017-09-06 00:00:00

abstract：BACKGROUND:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...

journal_title：Genome biology

authors： Rousseau M,Ferraiuolo MA,Crutchley JL,Wang XQ,Miura H,Blanchette M,Dostie J

更新日期：2014-04-30 00:00:00

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

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

更新日期：2019-02-26 00:00:00

abstract：BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...

journal_title：Genome biology

authors： Prins BP,Mead TJ,Brody JA,Sveinbjornsson G,Ntalla I,Bihlmeyer NA,van den Berg M,Bork-Jensen J,Cappellani S,Van Duijvenboden S,Klena NT,Gabriel GC,Liu X,Gulec C,Grarup N,Haessler J,Hall LM,Iorio A,Isaacs A,Li-Gao R,

更新日期：2018-07-17 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：BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...

journal_title：Genome biology

authors： Pushker R,Mira A,Rodríguez-Valera F

更新日期：2004-01-01 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：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

journal_title：Genome biology

authors： van der Graaff E,Laux T,Rensing SA

更新日期：2009-01-01 00:00:00

abstract：:Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

journal_title：Genome biology

authors： Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

更新日期：2011-01-01 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：:Ever since DNA microarrays were first applied to the quantitation of RNA levels, there has been considerable interest in generating a protein homolog that can be used to assay cellular protein expression. A recent paper describes the first microarray that can be used for such protein profiling. ...

journal_title：Genome biology

authors： Tomlinson IM,Holt LJ

更新日期：2001-01-01 00:00:00

abstract：:Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

journal_title：Genome biology

authors： Clark KJ,Carlson DF,Fahrenkrug SC

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...

journal_title：Genome biology

authors： Badouin H,Velt A,Gindraud F,Flutre T,Dumas V,Vautrin S,Marande W,Corbi J,Sallet E,Ganofsky J,Santoni S,Guyot D,Ricciardelli E,Jepsen K,Käfer J,Berges H,Duchêne E,Picard F,Hugueney P,Tavares R,Bacilieri R,Rustenh

更新日期：2020-09-07 00:00:00

abstract：BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

journal_title：Genome biology

authors： Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

更新日期：2009-01-01 00:00:00

abstract：:We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by

journal_title：Genome biology

authors： Ameur A,Wetterbom A,Feuk L,Gyllensten U

更新日期：2010-01-01 00:00:00

abstract：:The telomeres that cap the ends of eukaryotic chromosomes serve a dual role in protecting the chromosome ends and in intracellular signaling for regulating cell proliferation. A complex of six telomere-associated proteins has been identified--the telosome or shelterin complex--that is crucial for both the maintenance ...

journal_title：Genome biology

authors： Xin H,Liu D,Songyang Z

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...

journal_title：Genome biology

authors： Notebaart RA,Kensche PR,Huynen MA,Dutilh BE

更新日期：2009-02-12 00:00:00

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

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

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...

journal_title：Genome biology

authors： Xia X,Kung AL

更新日期：2009-01-01 00:00:00

abstract：:Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies. The availability of exome and genome da...

journal_title：Genome biology

authors： Katsanis N

更新日期：2016-11-17 00:00:00

abstract：BACKGROUND:The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto...

journal_title：Genome biology

authors： Blasius M,Forment JV,Thakkar N,Wagner SA,Choudhary C,Jackson SP

更新日期：2011-08-18 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：BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

journal_title：Genome biology

authors： Henry CS,Zinner JF,Cohoon MP,Stevens RL

更新日期：2009-01-01 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：:We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold...

journal_title：Genome biology

authors： Szpak M,Mezzavilla M,Ayub Q,Chen Y,Xue Y,Tyler-Smith C

更新日期：2018-01-17 00:00:00