VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 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：:The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

journal_title：Genome biology

authors： Gardiner K,Davisson M

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role for aberrant transcriptional regulation in AML pathophysiology. Although several transcription factors (TFs) involved in myeloid ...

journal_title：Genome biology

authors： Chang LW,Payton JE,Yuan W,Ley TJ,Nagarajan R,Stormo GD

更新日期：2008-01-01 00:00:00

abstract：:Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of communit...

journal_title：Genome biology

authors： DeMaere MZ,Darling AE

更新日期：2019-02-26 00:00:00

abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

journal_title：Genome biology

authors： Prakash A,Bateman A

更新日期：2015-04-30 00:00:00

abstract：:A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...

journal_title：Genome biology

authors： Fordyce P,Ingolia N

更新日期：2011-01-01 00:00:00

abstract：:The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence. ...

journal_title：Genome biology

authors： Ashburner M,Kyriacou CP

更新日期：2006-01-01 00:00:00

abstract：:Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...

journal_title：Genome biology

authors： Dimmer KS,Rapaport D

更新日期：2008-01-01 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：:Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected...

journal_title：Genome biology

authors： Wu W,Ji P,Zhao F

更新日期：2020-04-28 00:00:00

abstract：:An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh. ...

journal_title：Genome biology

authors： Mendenhall EM,Bernstein BE

更新日期：2012-01-27 00:00:00

abstract：BACKGROUND:Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on tra...

journal_title：Genome biology

authors： Thieme M,Lanciano S,Balzergue S,Daccord N,Mirouze M,Bucher E

更新日期：2017-07-07 00:00:00

abstract：:Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...

journal_title：Genome biology

authors： Joung JK,Voytas DF,Kamens J

更新日期：2015-11-20 00:00:00

abstract：:The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...

journal_title：Genome biology

authors： Barberán-Soler S,Vo JM,Hogans RE,Dallas A,Johnston BH,Kazakov SA

更新日期：2018-09-03 00:00:00

abstract：BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...

journal_title：Genome biology

authors： Hastie T,Tibshirani R,Botstein D,Brown P

更新日期：2001-01-01 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：:Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

journal_title：Genome biology

authors： Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...

journal_title：Genome biology

authors： Concia L,Veluchamy A,Ramirez-Prado JS,Martin-Ramirez A,Huang Y,Perez M,Domenichini S,Rodriguez Granados NY,Kim S,Blein T,Duncan S,Pichot C,Manza-Mianza D,Juery C,Paux E,Moore G,Hirt H,Bergounioux C,Crespi M,Mahfouz

更新日期：2020-04-29 00:00:00

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

authors： Wu J,Xie X

更新日期：2006-01-01 00:00:00

abstract：:Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

journal_title：Genome biology

authors： Gopal S,Awadalla S,Gaasterland T,Cross GA

更新日期：2005-01-01 00:00:00

abstract：:Precise and effective genome-editing tools are essential for functional genomics and gene therapy. Targeting nucleases have been successfully used to edit genomes. However, whole-locus or element-specific deletions abolishing transcript expression have not previously been reported. Here, we show heritable targeting of...

journal_title：Genome biology

authors： Lim S,Wang Y,Yu X,Huang Y,Featherstone MS,Sampath K

更新日期：2013-07-01 00:00:00

abstract：:The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

journal_title：Genome biology

authors： Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

更新日期：2015-01-22 00:00:00

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

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

abstract：:Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...

journal_title：Genome biology

authors： Sboner A,Mu XJ,Greenbaum D,Auerbach RK,Gerstein MB

更新日期：2011-08-25 00:00:00

abstract：BACKGROUND:Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major c...

journal_title：Genome biology

authors： Li Q,Tjong H,Li X,Gong K,Zhou XJ,Chiolo I,Alber F

更新日期：2017-07-31 00:00:00

abstract：:Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. ...

journal_title：Genome biology

authors： Kearsey S

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation. RESULTS:Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a pro...

journal_title：Genome biology

authors： Choi JK,Bae JB,Lyu J,Kim TY,Kim YJ

更新日期：2009-01-01 00:00:00

abstract：:Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

journal_title：Genome biology

authors： Bacher R,Kendziorski C

更新日期：2016-04-07 00:00:00

abstract：:Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome. ...

journal_title：Genome biology

authors： Morris DR

更新日期：2009-01-01 00:00:00