The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex.

abstract：BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

journal_title：Genome biology

authors： Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

更新日期：2013-03-25 00:00:00

abstract：BACKGROUND:It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromer...

journal_title：Genome biology

authors： Bulazel KV,Ferreri GC,Eldridge MD,O'Neill RJ

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...

journal_title：Genome biology

authors： Conrad TM,Joyce AR,Applebee MK,Barrett CL,Xie B,Gao Y,Palsson BØ

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00

abstract：:The first highly specific knockouts of a microRNA, miR155, in mice result in multiple defects in adaptive immunity, and also show the feasibility of investigating at least some microRNAs by gene knockout. ...

journal_title：Genome biology

authors： Moffett HF,Novina CD

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...

journal_title：Genome biology

authors： Ruotolo R,Marchini G,Ottonello S

更新日期：2008-04-07 00:00:00

abstract：:A report on the 64th annual American Society of Human Genetics meeting held in San Diego, USA, 18-22 October, 2014. ...

journal_title：Genome biology

authors： Reppell M,Koch E,Peter BM,Novembre J

更新日期：2014-12-17 00:00:00

abstract：:As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

journal_title：Genome biology

authors： Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...

journal_title：Genome biology

authors： Brownstein CA,Beggs AH,Homer N,Merriman B,Yu TW,Flannery KC,DeChene ET,Towne MC,Savage SK,Price EN,Holm IA,Luquette LJ,Lyon E,Majzoub J,Neupert P,McCallie D Jr,Szolovits P,Willard HF,Mendelsohn NJ,Temme R,Finkel R

更新日期：2014-03-25 00:00:00

abstract：BACKGROUND:Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS:A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped ...

journal_title：Genome biology

authors： Dalrymple BP,Kirkness EF,Nefedov M,McWilliam S,Ratnakumar A,Barris W,Zhao S,Shetty J,Maddox JF,O'Grady M,Nicholas F,Crawford AM,Smith T,de Jong PJ,McEwan J,Oddy VH,Cockett NE,International Sheep Genomics Consortium.

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

journal_title：Genome biology

authors： Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

更新日期：2020-02-20 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：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

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

abstract：BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

journal_title：Genome biology

authors： Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

更新日期：2015-04-16 00:00:00

abstract：BACKGROUND:Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. RESULTS:He...

journal_title：Genome biology

authors： Mak KS,Burdach J,Norton LJ,Pearson RC,Crossley M,Funnell AP

更新日期：2014-04-30 00:00:00

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

authors： Marques AC,Tan J,Ponting CP

更新日期：2011-11-21 00:00:00

abstract：BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

journal_title：Genome biology

authors： Tamames J,Moya A,Valencia A

更新日期：2007-01-01 00:00:00

abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...

journal_title：Genome biology

authors： Nadeau JH

更新日期：2015-07-11 00:00:00

abstract：BACKGROUND:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...

journal_title：Genome biology

authors： González V,Bustos P,Ramírez-Romero MA,Medrano-Soto A,Salgado H,Hernández-González I,Hernández-Celis JC,Quintero V,Moreno-Hagelsieb G,Girard L,Rodríguez O,Flores M,Cevallos MA,Collado-Vides J,Romero D,Dávila G

更新日期：2003-01-01 00:00:00

abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

journal_title：Genome biology

authors： Le Thomas A,Tóth KF,Aravin AA

更新日期：2014-01-27 00:00:00

abstract：:Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...

journal_title：Genome biology

authors： Cui X,Churchill GA

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...

journal_title：Genome biology

authors： Wu X,Xiao S,Zhang M,Yang L,Zhong J,Li B,Li F,Xia X,Li X,Zhou H,Liu D,Huang N,Yang X,Xiao F,Zhang N

更新日期：2021-01-14 00:00:00

abstract：BACKGROUND:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities,...

journal_title：Genome biology

authors： Tarallo R,Giurato G,Bruno G,Ravo M,Rizzo F,Salvati A,Ricciardi L,Marchese G,Cordella A,Rocco T,Gigantino V,Pierri B,Cimmino G,Milanesi L,Ambrosino C,Nyman TA,Nassa G,Weisz A

更新日期：2017-10-06 00:00:00

abstract：BACKGROUND:Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammali...

journal_title：Genome biology

authors： Cardone MF,Alonso A,Pazienza M,Ventura M,Montemurro G,Carbone L,de Jong PJ,Stanyon R,D'Addabbo P,Archidiacono N,She X,Eichler EE,Warburton PE,Rocchi M

更新日期：2006-01-01 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：BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resista...

journal_title：Genome biology

authors： Nordlund J,Bäcklin CL,Wahlberg P,Busche S,Berglund EC,Eloranta ML,Flaegstad T,Forestier E,Frost BM,Harila-Saari A,Heyman M,Jónsson OG,Larsson R,Palle J,Rönnblom L,Schmiegelow K,Sinnett D,Söderhäll S,Pastinen T,Gusta

更新日期：2013-09-24 00:00:00

abstract：BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...

journal_title：Genome biology

authors： Malone JH,Cho DY,Mattiuzzo NR,Artieri CG,Jiang L,Dale RK,Smith HE,McDaniel J,Munro S,Salit M,Andrews J,Przytycka TM,Oliver B

更新日期：2012-04-24 00:00:00

abstract：:The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

journal_title：Genome biology

authors： Schlueter SD,Wilkerson MD,Dong Q,Brendel V

更新日期：2006-01-01 00:00:00

abstract：:High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...

journal_title：Genome biology

authors： Levine M

更新日期：2008-01-01 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