The plasticity of the grapevine berry transcriptome.

abstract：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

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

authors： Gibson TJ

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

journal_title：Genome biology

authors： Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

更新日期：2020-08-26 00:00:00

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

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

更新日期：2006-01-01 00:00:00

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

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

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...

journal_title：Genome biology

authors： Zhou L,Tian S,Qin G

更新日期：2019-08-06 00:00:00

abstract：:Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...

journal_title：Genome biology

authors： Wilkerson MD,Schlueter SD,Brendel V

更新日期：2006-01-01 00:00:00

abstract：:By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle. ...

journal_title：Genome biology

authors： Giorgetti L,Servant N,Heard E

更新日期：2013-12-24 00:00:00

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

authors： Gabaldón T

更新日期：2008-10-30 00:00:00

abstract：BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

journal_title：Genome biology

authors： Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

更新日期：2021-01-04 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：:The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...

journal_title：Genome biology

authors： McHale L,Tan X,Koehl P,Michelmore RW

更新日期：2006-01-01 00:00:00

abstract：:Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...

journal_title：Genome biology

authors： Li Y,Park AI,Mou H,Colpan C,Bizhanova A,Akama-Garren E,Joshi N,Hendrickson EA,Feldser D,Yin H,Anderson DG,Jacks T,Weng Z,Xue W

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 ben...

journal_title：Genome biology

authors： Lim EL,Trinh DL,Scott DW,Chu A,Krzywinski M,Zhao Y,Robertson AG,Mungall AJ,Schein J,Boyle M,Mottok A,Ennishi D,Johnson NA,Steidl C,Connors JM,Morin RD,Gascoyne RD,Marra MA

更新日期：2015-01-29 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:Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced follow...

journal_title：Genome biology

authors： Han R,Li L,Ugalde AP,Tal A,Manber Z,Barbera EP,Chiara VD,Elkon R,Agami R

更新日期：2018-08-17 00:00:00

abstract：BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...

journal_title：Genome biology

authors： Usui K,Katayama S,Kanamori-Katayama M,Ogawa C,Kai C,Okada M,Kawai J,Arakawa T,Carninci P,Itoh M,Takio K,Miyano M,Kidoaki S,Matsuda T,Hayashizaki Y,Suzuki H

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanis...

journal_title：Genome biology

authors： Shamseldin HE,Masuho I,Alenizi A,Alyamani S,Patil DN,Ibrahim N,Martemyanov KA,Alkuraya FS

更新日期：2016-09-27 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：:Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

journal_title：Genome biology

authors： Johnson CH

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

journal_title：Genome biology

authors： Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

更新日期：2017-05-31 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：BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...

journal_title：Genome biology

authors： Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial s...

journal_title：Genome biology

authors： Hogg JS,Hu FZ,Janto B,Boissy R,Hayes J,Keefe R,Post JC,Ehrlich GD

更新日期：2007-01-01 00:00:00

abstract：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 00:00:00

abstract：: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. ...

journal_title：Genome biology

authors： Modesti M,Kanaar R

更新日期：2001-01-01 00:00:00

abstract：:Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...

journal_title：Genome biology

authors： Shahryary Y,Symeonidi A,Hazarika RR,Denkena J,Mubeen T,Hofmeister B,van Gurp T,Colomé-Tatché M,Verhoeven KJF,Tuskan G,Schmitz RJ,Johannes F

更新日期：2020-10-06 00:00:00

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

authors： Groza C,Kwan T,Soranzo N,Pastinen T,Bourque G

更新日期：2020-05-25 00:00:00

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

authors： Yeung KY,Bumgarner RE

更新日期：2003-01-01 00:00:00

abstract：:A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...

journal_title：Genome biology

authors： Ming R,Man Wai C

更新日期：2015-01-31 00:00:00