Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes.

abstract：BACKGROUND:Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all ly...

journal_title：Genome biology

authors： Bakker B,Taudt A,Belderbos ME,Porubsky D,Spierings DC,de Jong TV,Halsema N,Kazemier HG,Hoekstra-Wakker K,Bradley A,de Bont ES,van den Berg A,Guryev V,Lansdorp PM,Colomé-Tatché M,Foijer F

更新日期：2016-05-31 00:00:00

abstract：:Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...

journal_title：Genome biology

authors： Swift S,Tucker A,Vinciotti V,Martin N,Orengo C,Liu X,Kellam P

更新日期：2004-01-01 00:00:00

abstract：:A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...

journal_title：Genome biology

authors： Havel JJ,Chan TA

更新日期：2015-03-31 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:There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS:The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expre...

journal_title：Genome biology

authors： Lin HY,Liu Q,Li X,Yang J,Liu S,Huang Y,Scanlon MJ,Nettleton D,Schnable PS

更新日期：2017-10-17 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：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：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform ...

journal_title：Genome biology

authors： Westoby J,Artemov P,Hemberg M,Ferguson-Smith A

更新日期：2020-03-23 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:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

journal_title：Genome biology

authors： Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

更新日期：2011-12-30 00:00:00

abstract：BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...

journal_title：Genome biology

authors： Li Z,Wang M,Lin K,Xie Y,Guo J,Ye L,Zhuang Y,Teng W,Ran X,Tong Y,Xue Y,Zhang W,Zhang Y

更新日期：2019-07-15 00:00:00

abstract：BACKGROUND:Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcriptional program essential for bone formation through genetic and epigenetic mechanisms. While individual Runx2 gene target...

journal_title：Genome biology

authors： Wu H,Whitfield TW,Gordon JA,Dobson JR,Tai PW,van Wijnen AJ,Stein JL,Stein GS,Lian JB

更新日期：2014-03-21 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:DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteocla...

journal_title：Genome biology

authors： de la Rica L,Rodríguez-Ubreva J,García M,Islam AB,Urquiza JM,Hernando H,Christensen J,Helin K,Gómez-Vaquero C,Ballestar E

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such...

journal_title：Genome biology

authors： Reece-Hoyes JS,Deplancke B,Shingles J,Grove CA,Hope IA,Walhout AJ

更新日期：2005-01-01 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：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：:The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a ...

journal_title：Genome biology

authors： Daron J,Slotkin RK

更新日期：2017-05-12 00:00:00

abstract：BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...

journal_title：Genome biology

authors： Siddiqui NU,Li X,Luo H,Karaiskakis A,Hou H,Kislinger T,Westwood JT,Morris Q,Lipshitz HD

更新日期：2012-02-20 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：BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

journal_title：Genome biology

authors： Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

更新日期：2019-08-01 00:00:00

abstract：BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

journal_title：Genome biology

authors： Huang M,Ding S,Wang H,Zhu X

更新日期：2008-01-01 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：:A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009. ...

journal_title：Genome biology

authors： Ivics Z

更新日期：2009-01-01 00:00:00

abstract：:A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...

journal_title：Genome biology

authors： Iwanicki MP,Brugge JS

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 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：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

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